Create new export modal

app/controllers/AnnotationIOController.scala

@@ -370,7 +370,8 @@ Expects:
                                           None,
                                           organizationName,
                                           Some(user),
-                                          taskOpt)
+                                          taskOpt,
+                                          skipVolumeData)
         temporaryFile = temporaryFileCreator.create()
         zipper = ZipIO.startZip(new BufferedOutputStream(new FileOutputStream(new File(temporaryFile.path.toString))))
         _ <- zipper.addFileFromEnumerator(name + ".nml", nmlStream)

app/models/annotation/nml/NmlWriter.scala

@@ -39,7 +39,8 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
                   volumeFilename: Option[String],
                   organizationName: String,
                   annotationOwner: Option[User],
-                  annotationTask: Option[Task]): Enumerator[Array[Byte]] = Enumerator.outputStream { os =>
+                  annotationTask: Option[Task],
+                  skipVolumeData: Boolean = false): Enumerator[Array[Byte]] = Enumerator.outputStream { os =>
     implicit val writer: IndentingXMLStreamWriter =
       new IndentingXMLStreamWriter(outputService.createXMLStreamWriter(os))
 
@@ -50,7 +51,8 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
                    volumeFilename,
                    organizationName,
                    annotationOwner,
-                   annotationTask)
+                   annotationTask,
+                   skipVolumeData)
       _ = os.close()
     } yield nml
   }
@@ -61,7 +63,8 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
             volumeFilename: Option[String],
             organizationName: String,
             annotationOwner: Option[User],
-            annotationTask: Option[Task])(implicit writer: XMLStreamWriter): Fox[Unit] =
+            annotationTask: Option[Task],
+            skipVolumeData: Boolean)(implicit writer: XMLStreamWriter): Fox[Unit] =
     for {
       _ <- Xml.withinElement("things") {
         for {
@@ -81,7 +84,8 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
             case _                     => ()
           }
           _ = volumeLayers.zipWithIndex.foreach {
-            case (volumeLayer, index) => writeVolumeThings(volumeLayer, index, volumeLayers.length == 1, volumeFilename)
+            case (volumeLayer, index) =>
+              writeVolumeThings(volumeLayer, index, volumeLayers.length == 1, volumeFilename, skipVolumeData)
           }
         } yield ()
       }
@@ -193,14 +197,21 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
   def writeVolumeThings(volumeLayer: FetchedAnnotationLayer,
                         index: Int,
                         isSingle: Boolean,
-                        volumeFilename: Option[String])(implicit writer: XMLStreamWriter): Unit =
-    Xml.withinElementSync("volume") {
-      writer.writeAttribute("id", index.toString)
-      writer.writeAttribute("location", volumeFilename.getOrElse(volumeLayer.volumeDataZipName(index, isSingle)))
-      volumeLayer.name.foreach(n => writer.writeAttribute("name", n))
-      volumeLayer.tracing match {
-        case Right(volumeTracing) => volumeTracing.fallbackLayer.foreach(writer.writeAttribute("fallbackLayer", _))
-        case _                    => ()
+                        volumeFilename: Option[String],
+                        skipVolumeData: Boolean)(implicit writer: XMLStreamWriter): Unit =
+    if (skipVolumeData) {
+      val nameLabel = volumeLayer.name.map(n => f"named $n ").getOrElse("")
+      writer.writeComment(
+        f"A volume layer $nameLabel(id = $index) was omitted here while downloading this annotation without volume data.")
+    } else {
+      Xml.withinElementSync("volume") {
+        writer.writeAttribute("id", index.toString)
+        writer.writeAttribute("location", volumeFilename.getOrElse(volumeLayer.volumeDataZipName(index, isSingle)))
+        volumeLayer.name.foreach(n => writer.writeAttribute("name", n))
+        volumeLayer.tracing match {
+          case Right(volumeTracing) => volumeTracing.fallbackLayer.foreach(writer.writeAttribute("fallbackLayer", _))
+          case _                    => ()
+        }
       }
     }
 

frontend/javascripts/admin/admin_rest_api.ts

@@ -874,11 +874,12 @@ export function convertToHybridTracing(
   });
 }
 
-export async function downloadNml(
+export async function downloadAnnotation(
   annotationId: string,
   annotationType: APIAnnotationType,
   showVolumeFallbackDownloadWarning: boolean = false,
   versions: Versions = {},
+  includeVolumeData: boolean = true,
 ) {
   const possibleVersionString = Object.entries(versions)
     .map(([key, val]) => `${key}Version=${val}`)
@@ -889,11 +890,14 @@ export async function downloadNml(
       timeout: 12000,
     });
   }
+  const skipVolumeDataString = includeVolumeData ? "" : "skipVolumeData=true";
+  const maybeAmpersand = possibleVersionString === "" && !includeVolumeData ? "" : "&";
 
-  const downloadUrl = `/api/annotations/${annotationType}/${annotationId}/download?${possibleVersionString}`;
+  const downloadUrl = `/api/annotations/${annotationType}/${annotationId}/download?${possibleVersionString}${maybeAmpersand}${skipVolumeDataString}`;
   const { buffer, headers } = await Request.receiveArraybuffer(downloadUrl, {
     extractHeaders: true,
   });
+
   // Using headers to determine the name and type of the file.
   const contentDispositionHeader = headers["content-disposition"];
   const filenameStartingPart = 'filename="';

frontend/javascripts/admin/job/job_list_view.tsx

@@ -174,6 +174,20 @@ class JobListView extends React.PureComponent<Props, State> {
           </Link>{" "}
         </span>
       );
+    } else if (
+      job.type === "infer_neurons" &&
+      job.organizationName &&
+      job.datasetName &&
+      job.layerName
+    ) {
+      return (
+        <span>
+          Neuron inferral for layer {job.layerName} of{" "}
+          <Link to={`/datasets/${job.organizationName}/${job.datasetName}/view`}>
+            {job.datasetName}
+          </Link>{" "}
+        </span>
+      );
     } else if (
       job.type === "materialize_volume_annotation" &&
       job.organizationName &&

frontend/javascripts/admin/project/project_list_view.tsx

@@ -29,7 +29,7 @@ import {
   deleteProject,
   pauseProject,
   resumeProject,
-  downloadNml,
+  downloadAnnotation,
   getTasks,
   getTaskType,
 } from "admin/admin_rest_api";
@@ -409,7 +409,7 @@ class ProjectListView extends React.PureComponent<PropsWithRouter, State> {
                       href="#"
                       onClick={async () => {
                         this.maybeShowNoFallbackDataInfo(project.id);
-                        await downloadNml(project.id, "CompoundProject");
+                        await downloadAnnotation(project.id, "CompoundProject");
                       }}
                       title="Download all Finished Annotations"
                       icon={<DownloadOutlined key="download-icon" />}

frontend/javascripts/admin/task/task_annotation_view.tsx

@@ -23,7 +23,7 @@ import {
   finishAnnotation,
   resetAnnotation,
   deleteAnnotation,
-  downloadNml,
+  downloadAnnotation,
 } from "admin/admin_rest_api";
 import FormattedDate from "components/formatted_date";
 import Toast from "libs/toast";
@@ -143,7 +143,7 @@ class TaskAnnotationView extends React.PureComponent<Props, State> {
             href="#"
             onClick={() => {
               const isVolumeIncluded = getVolumeDescriptors(annotation).length > 0;
-              return downloadNml(annotation.id, "Task", isVolumeIncluded);
+              return downloadAnnotation(annotation.id, "Task", isVolumeIncluded);
             }}
             icon={<DownloadOutlined />}
           >

frontend/javascripts/admin/task/task_list_view.tsx

@@ -19,7 +19,7 @@ import _ from "lodash";
 import features from "features";
 import { AsyncLink } from "components/async_clickables";
 import type { APITask, APITaskType } from "types/api_flow_types";
-import { deleteTask, getTasks, downloadNml } from "admin/admin_rest_api";
+import { deleteTask, getTasks, downloadAnnotation } from "admin/admin_rest_api";
 import { formatTuple, formatSeconds } from "libs/format_utils";
 import { handleGenericError } from "libs/error_handling";
 import FormattedDate from "components/formatted_date";
@@ -418,7 +418,7 @@ class TaskListView extends React.PureComponent<Props, State> {
                       href="#"
                       onClick={() => {
                         const includesVolumeData = task.type.tracingType !== "skeleton";
-                        return downloadNml(task.id, "CompoundTask", includesVolumeData);
+                        return downloadAnnotation(task.id, "CompoundTask", includesVolumeData);
                       }}
                       title="Download all Finished Annotations"
                       icon={<DownloadOutlined />}

frontend/javascripts/admin/tasktype/task_type_list_view.tsx

@@ -9,7 +9,7 @@ import * as React from "react";
 import _ from "lodash";
 import { AsyncLink } from "components/async_clickables";
 import type { APITaskType } from "types/api_flow_types";
-import { getTaskTypes, deleteTaskType, downloadNml } from "admin/admin_rest_api";
+import { getTaskTypes, deleteTaskType, downloadAnnotation } from "admin/admin_rest_api";
 import { handleGenericError } from "libs/error_handling";
 import LinkButton from "components/link_button";
 import Persistence from "libs/persistence";
@@ -287,7 +287,11 @@ class TaskTypeListView extends React.PureComponent<Props, State> {
                     href="#"
                     onClick={() => {
                       const includesVolumeData = taskType.tracingType !== "skeleton";
-                      return downloadNml(taskType.id, "CompoundTaskType", includesVolumeData);
+                      return downloadAnnotation(
+                        taskType.id,
+                        "CompoundTaskType",
+                        includesVolumeData,
+                      );
                     }}
                     title="Download all Finished Annotations"
                     icon={<DownloadOutlined />}

frontend/javascripts/dashboard/dashboard_task_list_view.tsx

@@ -28,7 +28,7 @@ import {
   finishTask,
   requestTask,
   peekNextTasks,
-  downloadNml,
+  downloadAnnotation,
 } from "admin/admin_rest_api";
 import { enforceActiveUser } from "oxalis/model/accessors/user_accessor";
 import { getSkeletonDescriptor } from "oxalis/model/accessors/skeletontracing_accessor";
@@ -272,7 +272,7 @@ class DashboardTaskListView extends React.PureComponent<PropsWithRouter, State>
               href="#"
               onClick={() => {
                 const isVolumeIncluded = getVolumeDescriptors(annotation).length > 0;
-                return downloadNml(annotation.id, "Task", isVolumeIncluded);
+                return downloadAnnotation(annotation.id, "Task", isVolumeIncluded);
               }}
               icon={<DownloadOutlined />}
             >

frontend/javascripts/dashboard/explorative_annotations_view.tsx

@@ -23,7 +23,7 @@ import {
   finishAnnotation,
   reOpenAnnotation,
   getCompactAnnotations,
-  downloadNml,
+  downloadAnnotation,
   getCompactAnnotationsForUser,
 } from "admin/admin_rest_api";
 import { formatHash } from "libs/format_utils";
@@ -240,7 +240,7 @@ class ExplorativeAnnotationsView extends React.PureComponent<Props, State> {
           <br />
           <AsyncLink
             href="#"
-            onClick={() => downloadNml(id, typ, hasVolumeTracing)}
+            onClick={() => downloadAnnotation(id, typ, hasVolumeTracing)}
             icon={<DownloadOutlined key="download" />}
           >
             Download

frontend/javascripts/messages.ts

@@ -105,7 +105,7 @@ Editing should be done in a single window only.
 
 In order to restore the current window, a reload is necessary.`,
   "react.rendering_error":
-    "Unfortunately, we encountered an error during rendering. We cannot guarantee that your work is persisted. Please reload the page and try again.",
+    "Unfortunately, webKnossos encountered an error during rendering. Your latest changes may not have been saved. Please reload the page to try again.",
   "save.leave_page_unfinished":
     "WARNING: You have unsaved progress that may be lost when hitting OK. Please click cancel, wait until the progress is saved and the save button displays a checkmark before leaving the page..",
   "save.failed": "Failed to save annotation. Retrying.",
@@ -293,6 +293,13 @@ instead. Only enable this option if you understand its effect. All layers will n
   "annotation.delete": "Do you really want to reset and cancel this annotation?",
   "annotation.was_edited": "Successfully updated annotation",
   "annotation.shared_teams_edited": "Successfully updated the sharing options for the annotation",
+  "annotation.download": "The following annotation data is available for download immediately.",
+  "annotation.export":
+    "Exporting this annotation as TIFF images will trigger a background job to prepare data for download. This may take a while depending on the size of your dataset as well as bounding box and layer selection. You can monitor the progress and start the download from the ",
+  "annotation.export_no_worker":
+    "This webKnossos instance is not configured to run TIFF export jobs on a dedicated background worker. To learn more about this feature please contact us at ",
+  "annotation.python_do_not_share":
+    "These snippets are pre-configured and contain your personal access token and annotation meta data. Do not share this information with anyone you do not trust!",
   "project.delete": "Do you really want to delete this project?",
   "project.increase_instances":
     "Do you really want to add one additional instance to all tasks of this project?",

frontend/javascripts/oxalis/default_state.ts

@@ -204,6 +204,7 @@ const defaultState: OxalisState = {
     activeTool: "MOVE",
     showDropzoneModal: false,
     showVersionRestore: false,
+    showDownloadModal: false,
     showShareModal: false,
     storedLayouts: {},
     isImportingMesh: false,

frontend/javascripts/oxalis/model/actions/ui_actions.ts

@@ -46,6 +46,12 @@ type SetThemeAction = {
   type: "SET_THEME";
   value: Theme;
 };
+
+type SetDownloadModalVisibilityAction = {
+  type: "SET_DOWNLOAD_MODAL_VISIBILITY";
+  visible: boolean;
+};
+
 type SetShareModalVisibilityAction = {
   type: "SET_SHARE_MODAL_VISIBILITY";
   visible: boolean;
@@ -61,6 +67,7 @@ export type UiAction =
   | SetToolAction
   | CycleToolAction
   | SetThemeAction
+  | SetDownloadModalVisibilityAction
   | SetShareModalVisibilityAction
   | SetBusyBlockingInfoAction;
 export const setDropzoneModalVisibilityAction = (
@@ -110,6 +117,14 @@ export const setThemeAction = (value: Theme): SetThemeAction => ({
   type: "SET_THEME",
   value,
 });
+
+export const setDownloadModalVisibilityAction = (
+  visible: boolean,
+): SetDownloadModalVisibilityAction => ({
+  type: "SET_DOWNLOAD_MODAL_VISIBILITY",
+  visible,
+});
+
 export const setShareModalVisibilityAction = (visible: boolean): SetShareModalVisibilityAction => ({
   type: "SET_SHARE_MODAL_VISIBILITY",
   visible,

frontend/javascripts/oxalis/model/reducers/ui_reducer.ts

@@ -78,6 +78,10 @@ function UiReducer(state: OxalisState, action: Action): OxalisState {
       });
     }
 
+    case "SET_DOWNLOAD_MODAL_VISIBILITY": {
+      return updateKey(state, "uiInformation", { showDownloadModal: action.visible });
+    }
+
     case "SET_SHARE_MODAL_VISIBILITY": {
       return updateKey(state, "uiInformation", {
         showShareModal: action.visible,

frontend/javascripts/oxalis/store.ts

@@ -438,6 +438,7 @@ export type BusyBlockingInfo = {
 type UiInformation = {
   readonly showDropzoneModal: boolean;
   readonly showVersionRestore: boolean;
+  readonly showDownloadModal: boolean;
   readonly showShareModal: boolean;
   readonly activeTool: AnnotationTool;
   readonly storedLayouts: Record<string, any>;